The oil reservoirs of the metamorphic rocks in Bohai Bay have geological characteristics such as low matrix porosity and permeability, developed natural microfractures, which result in the injection water rapidly advancing along fractures, a fast increase in the water content, and difficulties in extracting the remaining oil. In order to reveal water channeling and the residual oil formation mechanisms in fractured low-permeability reservoirs and solve the water channeling problem, we first analyzed the reservoir development status, then studied the formation mechanism of residual oil using a microfluidic chip device, and formed a method of hierarchical control to effectively control the water channeling problem of fractured reservoirs and maximize the displacement of residual oil. The results show that (1) Due to the low permeability of the reservoir matrix, a large amount of injected water flows along the fracture channel, which leads to the long-term high water cut of some oil wells and the retention of a large amount of crude oil in the matrix. (2) The results of microfluidic experiments show that the distribution of residual oil after water flooding mainly includes five types: blind end of the pore throat, columnar, cluster, flake and film, and residual oil. Among them, sheet-like and clustered residual oil are dominant, accounting for 75~85% and 10~13%, respectively. (3) Based on the characteristics of fracture development in buried-hill reservoirs, a hierarchical control technology of “gel particle + liquid crosslinked gel system” is established. The field application effect predicted that the input–output ratio was 1:3. This study provides a reference for the comprehensive treatment of water channeling in the same type of offshore fractured low-permeability metamorphic rock reservoirs.